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Wednesday, November 30, 2016

Vilified in biblical texts and even ridiculed by Iggy Pop, the Iron Age pagan seafarers known as the Philistines were basically the East Mediterranean version of the Vikings, except apparently much smaller:

Relatively short average heights for people buried at Ashkelon — about 5 feet, 1 inch for men and 4 feet, 10 inches for women — also fit a scenario of biological stress, Fox said. Short stature and minimal height differences between men and women occur with population-wide stresses such as malnutrition, she said.
...
The Philistines were a famously combative crowd. Archaeologist Eric Meyers of Duke University, who was not a member of the Ashkelon team, wondered if at least some of those buried at Ashkelon had been killed in battles or fights. But no head injuries or other skeletal signs of violent encounters appeared among the dead at Ashkelon, Fox said. Neither did any skeletons contain evidence of tumors or cancers.
If DNA can be extracted from the Ashkelon skeletons, scientists may get a glimpse of where the Philistines originally came from. Evolutionary geneticist Johannes Krause of the Max Planck Institute for the Science of Human History in Jena, Germany, is currently directing efforts to retrieve genetic sequences from the Ashkelon bones.

Saturday, November 26, 2016

It's been a pretty big year. Not as big as many of us had hoped for, but there's still a few more weeks till 2017, so who knows what will happen?
In any case, for me 2016 will be the year in which we finally saw hard data - courtesy of Lazaridis et al. and Broushaki at al. - that crossed off the territory of present-day Iran from the list of potential Proto-Indo-European (PIE) homelands.
Now, it's true, Lazaridis et al. and Broushaki et al. were somewhat vague in what their data meant in this context, and indeed, both sets of authors left open the possibility that what is now Iran might prove to be the PIE homeland. However, their data left no doubt: look elsewhere for the PIE Urheimat.
Why? Here it is, in point form, as simply as I can put it:

- the Mesolithic and Neolithic peoples of the Zagros range and South Caspian region were highly distinct both in terms of genome-wide genetic structure and uniparental markers, and clearly only contributed meaningful gene flow to South Asia, not to Europe or Anatolia
- after the descendants of Neolithic farmers from the Zagros range, or at least their very close relatives, migrated to South Asia, the territory of present-day Iran, as per the data in Lazaridis et al. and Broushaki et al., saw waves of migrations from the west and north that dramatically shifted the population structure of the region, bringing it closer in this respect to the Levant and Europe
- most of the Neolithic samples from Iran in Lazaridis et al. and Broushaki et al. came from near the proto-Elamite homeland in the Kor River basin in central Fars, which strongly suggests that their close relatives who streamed into South Asia were not Indo-Europeans, but rather speakers of languages closely related to Elamite
- even though Lazaridis et al. successfully modeled Early/Middle Bronze Age steppe populations, including Yamnaya, as largely of Iran Chalcolithic origin, this appeared to be a coincidence, because the Chalcolithic samples from Iran showed fairly typical South Caspian uniparental markers, such as Y-chromosome haplogroups J and G1 and mitochondrial (mtDNA) haplogroup U7, which are conspicuous by their absence from an exceptionally wide range of Bronze Age steppe samples.

I do realize that many readers won't accept these arguments for emotional reasons, because the PIE homeland debate is an emotional one for a lot of people. Nevertheless, if you decide to argue with me in the comments, make sure you have a coherent argument.
Actually, the territory of present-day Iran has never been a serious contender in the PIE homeland debate. This is something that many Iranian scholars will freely admit.
Not only was central Fars the proto-Elamite homeland, but much of what is now western Iran was the stomping ground of the Hurrians. The Indo-Europeans, in the form of Indo-Iranians such as the Medes, only got there late in the game, in all likelihood from the Eurasian steppes.
But a lot of newbies to the PIE debate don't know this, or they don't want to know it. I guess to them, Iran makes sense because it's in between Europe and South Asia? Or maybe it's the fact that the word Iran is kind of similar to the word Aryan? No idea, really, but like I say, it's now all over.
See also...
A homeland, but not the homelandZarathushtra and his steppe posseThe story of mtDNA haplogroup U7

Thursday, November 24, 2016

The AJHG has a new open access paper on the population history of Chad. It lays out a reasonable hypothesis for the sources and timing of Eurasian gene flow into north central Africa. Just wondering, though, if the authors considered the possibility that R1b-V88 may have expanded into Africa from Iberia? After all, the oldest instance of a probable R1b-V88 to date is from an Iberian Early Neolithic sample (ID I0410, Els Trocs, Spain, Haak et al. 2015). But I don't have a strong opinion on the issue at the moment. From the paper (emphasis is mine):

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750–7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700–7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%–30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.
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It is important to note that in this work we inevitably invoke Occam’s razor to support the simplest model consistent with our data; the history of the populations studied here, including the time and sources of the Eurasian admixture in Africa, could be more complex. aDNA from Chad and neighboring regions remains a challenge given the poor DNA preservation in hot climates, but future successful efforts in aDNA research could provide additional insights and reveal additional complexities not considered by the modern-DNA-based models favored here.

Saturday, November 12, 2016

I've redesigned and streamlined my Principal Component Analysis (PCA) plot of West Eurasia in anticipation of the arrival of many more ancient samples. Rumor has it we'll not only get stuff from the Balkans, but also finally from the steppes north of the Black Sea and South Asia.
I'd say my new plot does a better job of highlighting relationships between the different prehistoric groups and population shifts across space and time. The datasheet is available here.

It should be pretty clear from this plot how the modern-day European gene pool came about. So I don't expect any major surprises when the new samples come in. Nevertheless, the wait is killing me, and many others I'm sure.
Update 13/11/2017: A year on, I've acquired many new samples and, as a result, streamlined the PCA some more, see...
Who's your (proto) daddy Western Europeans?

Monday, November 7, 2016

The Max Planck Institute for the Science of Human History is holding the Human Dispersals in the Late Pleistocene - Interdisciplinary Approaches Towards Understanding the Worldwide Expansion of Homo sapiens conference this week. The conference web page and abstract book are here.

The abstract below from Stephan Schiffels is very interesting. It reminds me of some of the discussions that we've had in the comments about potential African ancestry in some Eurasians that might be hiding due to a lack of relevant ancient African samples (for instance, see here).

When and how modern humans left the African continent is still a debated question. Recently, three projects have analysed new genetic data from modern populations in Papua New Guinea and Australia, which has provided new insights on this topic. I will present analyses from one of these publications (Malaspinas et al. 2016), and compare results with findings from the two other projects (Mallick et al. 2016, Pagani et al. 2016). Here, we used MSMC2, a novel computational framework to analyse the distribution of times to the most recent common ancestor along multiple sequences. We find that all non-African populations that we analysed, including Australians, experienced a very similar population bottleneck in the past, consistent with only one out-of-Africa migration for all extant non-African populations. At the same time, we find evidence that some African populations are more distantly related to Australians than to Eurasian populations, and we show that this result is robust to haplotype phasing errors and archaic introgression. We interpret our result as evidence for gene flow between some Africans and Eurasians after the initial split, which is also consistent with results from other population genetic methods. Our analysis suggests that in order to understand human dispersal out of Africa, we need to better understand ancient population substructure within Africa, which is an important direction for future research.

Stephan Schiffels, Analysing Australian genomes to learn about early modern human dispersal out of Africa, Human Dispersals in the Late Pleistocene - Interdisciplinary Approaches Towards Understanding the Worldwide Expansion of Homo sapiens 2016 conference abstract

Friday, November 4, 2016

I've built up a pretty good record over the past couple of years of pre-empting results that eventually show up in high end scientific journals.
Here's another major finding that you'll see at some point in Nature or Science: in present-day India upper caste membership is strongly associated with Eneolithic/Bronze Age steppe-related ancestry, while low caste membership and Dravidian languages are strongly associated with indigenous South Asian and Zagros Neolithic-related ancestry.
As far as I can see, with my somewhat limited dataset, the best way to show this is by plotting D-stats of the form D(Outgroup;Samara_Eneolithic)(Onge;X) versus D(Outgroup;Iran_Neolithic)(Onge;X). The relevant datasheet is available here.

Like I say, my dataset is still not great for this type of analysis, but the results are very striking and I have no doubt that they will be confirmed with more comprehensive sampling of Indian populations.
If they are confirmed, this will probably mean three things: 1) the caste system was introduced into the Indian subcontinent from the Eurasian steppe after the demise of the Chalcolithic Harappan civilization, 2) Zagros Neolithic farmers and closely related Neolithic/Chalcolithic populations of South Asia were not Indo-European-speaking, 3) like the caste system, Indo-Aryan (and thus Indo-European) languages were introduced into the Indian subcontinent from the Eurasian steppe after the Chalcolithic.
See also...
The peopling of South Asia: an illustrated guide